Chromosome Number: 2n=24
Quercus Portal - a genetic and genomic web resource for Quercus
The following browser provides a list of biomaterials associated with this organism.
Below is a list of transcriptomes available for Quercus alba. Click the transcriptome name for further details.
Mapping PopulationLocations: University of Tennessee, Ames Plantation in Ames, TN and East Tennessee State Nursery Principal Investigators: Scott Schlarbaum (University of Tennessee), Oliver Gailing (Michigan Tech)
A White Oak population that has been under development for many years at the Ame's Plantation (University of Tennessee). The plantation is being maintained by the UT Tree Improvement Program, including mowing and is protected against deer by electric fence and rabbits by tree shelters or mesh. Dr. Gailing has analyzed 200 trees in the population and found 50 full-sibling trees. Assuming the same rate of detection, the plantation currently contains between 200-250 full siblings. Approximately 200 seedlings from the mother tree were grown at the East Tennessee State Nursery in 2013. They were lifted and containerized for future sampling.
Please contact us for more information or if you are interested in utilizing this population for research. Genotype and phenotype information will be posted here when publicly available.
Predicted SSRs (genomic)Publication: Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PloS one. 2015 Dec 23;10(12):e0145031.
In order to develop SSR resources for ten important North American hardwood tree species, we individually barcoded and multiplex sequenced DNA from ten hardwood forest tree species using short reads produced from an Illumina HiSeq. Raw reads can be downloaded from the NCBI short read archive, project SRP021923. Bioinformatic processing included trimming, assembly, SSR identification and primer design, processing details including scripts are available. Statistics (combination of two sequenced libraries):
Confirmed Polymorphic SSRsJohn Carlson at Pennsylvania State University screened a subset of the above predicted SSRs.
Twelve white oaks were collected, consisting of the two parents of a mapping population and ten unrelated samples from the Pennsylvania State University arboretum (University Park, PA). DNA was extracted using a modified CTAB method, and DNA quality was assessed on 1% agarose gels. Species primer sets were tested against all collected genotypes within a species with a PCR reaction mixture containing between 4-6 ng DNA per reaction volume, and PCR cycles as follows: 95°C-5 min, 35 cycles of 95°C- 30s, 60°C-45s, 72°C-1 min, and a final 72°C-10 min. Both amplification and polymorphism were detected on 2% agarose gels stained with 0.05% (w/v) ethidium bromide. Polymorphism was estimated based on band width.
Of the 100 tested SSRs, 44 successfully amplified and 22 were found to be polymorphic.